2PYX | pdb_00002pyx

Crystal structure of tryptophan halogenase (YP_750003.1) from Shewanella frigidimarina NCIMB 400 at 1.50 A resolution

X-RAY DIFFRACTION

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Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	7.2	277	NANODROP, 0.2M Na Tartrate, 20.0% PEG 3350, No Buffer pH 7.2, VAPOR DIFFUSION, SITTING DROP, temperature 277K

Crystal Properties
Matthews coefficient	Solvent content
2.7	54.43

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 97.545	α = 90
b = 109.613	β = 90
c = 120.036	γ = 90

Symmetry
Space Group	P 21 21 21

Diffraction

Diffraction Experiment
ID #	Crystal ID	Scattering Type	Data Collection Temperature	Detector	Detector Type	Details	Collection Date	Monochromator	Protocol
1	1	x-ray	100	CCD	MARMOSAIC 325 mm CCD	Flat mirror (vertical focusing)	2007-04-30	M	MAD

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SSRL BEAMLINE BL11-1	0.91837, 0.97916, 0.97885	SSRL	BL11-1

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	R Sym I (Observed)	Net I Over Average Sigma (I)	Redundancy	Number Reflections (All)	Number Reflections (Observed)	Observed Criterion Sigma (F)	Observed Criterion Sigma (I)	B (Isotropic) From Wilson Plot
1	1.5	29.775	89.9	0.064	0.064	6.7	3.3		184436			14.91

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	R-Sym I (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.5	1.54	50.8		0.313	0.313	2	2.1	7554

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Resolution (High)	Resolution (Low)	Number Reflections (Observed)	Number Reflections (R-Free)	Percent Reflections (Observed)	R-Factor (Observed)	R-Work (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MAD	THROUGHOUT	1.5	29.775	184358	9258	89.84	0.153	0.151	0.15	0.181	0.18	RANDOM	14.04

Temperature Factor Modeling
Anisotropic B[1][1]	Anisotropic B[1][2]	Anisotropic B[1][3]	Anisotropic B[2][2]	Anisotropic B[2][3]	Anisotropic B[3][3]
-0.45			0.33		0.11

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	40.335
r_dihedral_angle_4_deg	12.078
r_dihedral_angle_3_deg	11.028
r_scangle_it	5.659
r_dihedral_angle_1_deg	5.549
r_scbond_it	3.803
r_mcangle_it	2.53
r_mcbond_it	1.709
r_angle_refined_deg	1.443
r_angle_other_deg	0.833
r_mcbond_other	0.43
r_symmetry_vdw_refined	0.299
r_symmetry_vdw_other	0.275
r_nbd_refined	0.216
r_nbd_other	0.178
r_nbtor_refined	0.178
r_xyhbond_nbd_refined	0.154
r_symmetry_hbond_refined	0.145
r_chiral_restr	0.092
r_nbtor_other	0.083
r_bond_refined_d	0.017
r_gen_planes_refined	0.007
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	8214
Nucleic Acid Atoms
Solvent Atoms	1587
Heterogen Atoms	67

Software

Software
Software Name	Purpose
REFMAC	refinement
PHENIX	refinement
SHELX	phasing
MolProbity	model building
SCALA	data scaling
PDB_EXTRACT	data extraction
MAR345	data collection
MOSFLM	data reduction
SHELXD	phasing
autoSHARP	phasing